659 lines
23 KiB
Python
659 lines
23 KiB
Python
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import gtk
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from fluents import dataset, logger, plots, workflow, fluents, project
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import geneontology
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from matplotlib.nxutils import points_inside_poly
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import matplotlib
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#from scipy import array, randn, log, ones, zeros
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from scipy import *
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from numpy import matlib
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import networkx
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import re
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import rpy
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EVIDENCE_CODES=[('IMP', 'Inferred from mutant phenotype'),
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('IGI', 'Inferred from genetic interaction'),
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('IPI', 'Inferred from physical interaction'),
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('ISS', 'Inferred from sequence or structure similarity'),
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('IDA', 'Inferred from direct assay'),
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('IEP', 'Inferred on expression pattern'),
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('IEA', 'Inferred from electronic annotation'),
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('TAS', 'Traceable author statement'),
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('NAS', 'Non-traceable author statement'),
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('ND', 'No biological data available'),
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('RCA', 'Inferred from reviewed computational analysis'),
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('IC', 'Inferred by curator')]
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DISTANCE_METRICS = [('resnik', 'Resnik'),
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('jiang', 'Jiang & Conrath'),
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('fussimeg', 'FuSSiMeG')]
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GO_DATA_DIR = '/home/einarr/data'
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evidence = None
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go = None
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class GoTermView (gtk.Frame):
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def __init__(self):
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gtk.Frame.__init__(self)
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tab = gtk.Table(2, 2, False)
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self._table = tab
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self._name = gtk.Label('')
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self._name.set_line_wrap(True)
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self._name.set_alignment(0, 0)
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name_label = gtk.Label('Name:')
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name_label.set_alignment(0, 0)
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tab.attach(name_label, 0, 1, 0, 1, gtk.FILL, gtk.FILL, 5, 5)
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tab.attach(self._name, 1, 2, 0, 1, gtk.FILL|gtk.EXPAND, gtk.FILL, 5, 5)
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self._def = gtk.TextBuffer()
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textview = gtk.TextView(self._def)
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textview.set_wrap_mode(gtk.WRAP_WORD)
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scrolled_window = gtk.ScrolledWindow()
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scrolled_window.add(textview)
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def_label = gtk.Label('Def:')
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def_label.set_alignment(0.0, 0.0)
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tab.attach(def_label, 0, 1, 1, 2, gtk.FILL, gtk.FILL, 5, 5)
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tab.attach(scrolled_window, 1, 2, 1, 2, gtk.FILL|gtk.EXPAND, gtk.FILL|gtk.EXPAND, 5, 5)
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self.add(tab)
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self.set_go_term(None)
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def set_go_term(self, term):
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if term:
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self.set_label(term['id'])
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self._name.set_text(term['name'])
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self._def.set_text(term['def'])
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else:
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self.set_label('GO Term')
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self._name.set_text('')
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self._def.set_text('')
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class GeneOntologyTree (gtk.HPaned):
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def __init__(self, network):
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gtk.HPaned.__init__(self)
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treemodel = geneontology.get_go_treestore(network)
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self._treemodel = treemodel
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self._tree_view = gtk.TreeView(treemodel)
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self._selected_terms = set()
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self._tree_view.set_fixed_height_mode(True)
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# Set up context menu
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self._context_menu = GoTermContextMenu(treemodel, self._tree_view)
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self._tree_view.connect('popup_menu', self._popup_menu)
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self._tree_view.connect('button_press_event', self._on_button_press)
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renderer = gtk.CellRendererText()
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go_column = gtk.TreeViewColumn('GO ID', renderer, text=0)
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go_column.set_sizing(gtk.TREE_VIEW_COLUMN_FIXED)
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go_column.set_fixed_width(200)
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go_column.set_resizable(True)
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self._tree_view.insert_column(go_column, 0)
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renderer = gtk.CellRendererToggle()
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renderer.set_property('activatable', True)
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renderer.connect('toggled', self._toggle_selected)
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renderer.set_active(True)
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renderer.set_property('mode', gtk.CELL_RENDERER_MODE_ACTIVATABLE)
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go_column = gtk.TreeViewColumn('T', renderer, active=2)
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go_column.set_fixed_width(20)
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go_column.set_sizing(gtk.TREE_VIEW_COLUMN_FIXED)
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go_column.set_resizable(True)
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self._tree_view.insert_column(go_column, 1)
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renderer = gtk.CellRendererText()
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go_column = gtk.TreeViewColumn('Name', renderer, text=1)
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go_column.set_fixed_width(200)
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go_column.set_sizing(gtk.TREE_VIEW_COLUMN_FIXED)
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go_column.set_resizable(True)
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self._tree_view.insert_column(go_column, 2)
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self._desc_view = GoTermView()
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self._tree_view.connect('cursor-changed', self._on_cursor_changed)
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scrolled_window = gtk.ScrolledWindow()
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scrolled_window.add(self._tree_view)
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self.add1(scrolled_window)
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self.add2(self._desc_view)
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self.show_all()
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def _on_cursor_changed(self, tree):
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path, col = self._tree_view.get_cursor()
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current = self._treemodel.get_iter(path)
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term = self._treemodel.get_value(current, 3)
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self._desc_view.set_go_term(term)
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##
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## GTK Callback functions
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##
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def _popup_menu(self, *rest):
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self.menu.popup(None, None, None, 0, 0)
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def _on_button_press(self, widget, event):
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path = widget.get_path_at_pos(int(event.x), int(event.y))
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iter = None
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if path:
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iter = self._treemodel.get_iter(path[0])
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obj = self._treemodel.get_value(iter, 3)
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else:
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obj = None
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self._context_menu.set_current_term(obj, iter)
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if event.button == 3:
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self._context_menu.popup(None, None, None, event.button, event.time)
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def _toggle_selected(self, renderer, path):
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iter = self._treemodel.get_iter(path)
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selected = self._treemodel.get_value(iter, 2)
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id = self._treemodel.get_value(iter, 0)
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self._treemodel.set_value(iter, 2, not selected)
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if selected:
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self._selected_terms.remove(id)
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else:
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self._selected_terms.add(id)
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class GoTermContextMenu (gtk.Menu):
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"""Context menu for GO terms in the gene ontology browser"""
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def __init__(self, treemodel, treeview):
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self._treemodel = treemodel
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self._treeview = treeview
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self._current_term = None
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self._current_iter = None
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gtk.Menu.__init__(self)
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# Popuplate tree
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self._expand_item = i = gtk.MenuItem('Expand')
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i.connect('activate', self._on_expand_subtree, treemodel, treeview)
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self.append(i)
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i.show()
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self._collapse_item = i = gtk.MenuItem('Collapse')
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i.connect('activate', self._on_collapse_subtree, treemodel, treeview)
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self.append(i)
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i.show()
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self._select_subtree_item = i = gtk.MenuItem('Select subtree')
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i.connect('activate', self._on_select_subtree, treemodel, treeview)
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self.append(i)
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i.show()
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def set_current_term(self, term, it):
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self._current_term = term
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self._current_iter = it
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def _on_expand_subtree(self, item, treemodel, treeview):
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path = treemodel.get_path(self._current_iter)
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treeview.expand_row(path, True)
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def _on_collapse_subtree(self, item, treemodel, treeview):
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treeview.collapse_row(treemodel.get_path(self._current_iter))
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def _on_select_subtree(self, item, treemodel, treeview):
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logger.log('notice', 'Selecting subtree from GO id: %s (%s)' %
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(self._current_term['id'], self._current_term['name']))
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ids = [x['id'] for x in networkx.bfs(go, self._current_term)]
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project.project.set_selection('go-terms', set(ids))
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class LoadGOFunction(workflow.Function):
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def __init__(self):
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workflow.Function.__init__(self, 'load-go', 'Load Gene Ontology')
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def run(self):
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global go
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if go:
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return
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go = geneontology.read_default_go()
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browser = GeneOntologyTree(go)
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label = gtk.Label('_Gene Ontology')
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label.set_use_underline(True)
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fluents.app['bottom_notebook'].append_page(browser, label)
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class LoadAnnotationsFunction(workflow.Function):
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def __init__(self):
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workflow.Function.__init__(self, 'load-go-ann', 'Load Annotations')
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self.annotations = None
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def run(self):
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global evidence
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f = open(GO_DATA_DIR + '/goa-condensed')
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ev_codes = f.readline().split()
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go_terms = []
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lines = f.readlines()
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m = zeros((len(lines), len(ev_codes)))
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for i, l in enumerate(lines):
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values = l.split()
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go_terms.append(values[0])
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for j, v in enumerate(values[1:]):
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m[i,j] = float(v.strip())
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d = dataset.Dataset(m,
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[['go-terms', go_terms], ['evidence', ev_codes]],
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name='GO evidence')
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evidence = d
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return [d]
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class GOWeightDialog(gtk.Dialog):
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def __init__(self):
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gtk.Dialog.__init__(self, 'GO Gene List Influence',
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None,
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gtk.DIALOG_MODAL | gtk.DIALOG_DESTROY_WITH_PARENT,
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(gtk.STOCK_OK, gtk.RESPONSE_OK,
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gtk.STOCK_CANCEL, gtk.RESPONSE_CANCEL))
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table = gtk.Table(2, 2)
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sim_lbl = gtk.Label('Similarity threshold: ')
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table.attach(sim_lbl, 0, 1, 0, 1)
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adjustment = gtk.Adjustment(0, 0, 10, 0.1, 1.0, 1.0)
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sim_spin = gtk.SpinButton(adjustment, 0.0, 2)
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table.attach(sim_spin, 1, 2, 0, 1)
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rank_lbl = gtk.Label('Rank threshold: ')
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table.attach(rank_lbl, 0, 1, 1, 2)
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rank_adj = gtk.Adjustment(0, 0, 10, 0.1, 1.0, 1.0)
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rank_spin = gtk.SpinButton(rank_adj, 0.0, 2)
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table.attach(rank_spin, 1, 2, 1, 2)
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sim_lbl.show()
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sim_spin.show()
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rank_lbl.show()
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rank_spin.show()
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table.show()
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self.vbox.add(table)
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self._sim_spin = sim_spin
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self._rank_spin = rank_spin
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def set_options(self, options):
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self._sim_spin.set_value(options['similarity_threshold'])
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self._rank_spin.set_value(options['rank_threshold'])
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def set_editable(self, editable):
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self._sim_spin.set_sensitive(editable)
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self._rank_spin.set_sensitive(editable)
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def update_options(self, options):
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options['similarity_threshold'] = self._sim_spin.get_value()
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options['rank_threshold'] = self._rank_spin.get_value()
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class DistanceToSelectionFunction(workflow.Function):
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def __init__(self):
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workflow.Function.__init__(self, 'dist-to-sel', 'Dist. to Selection')
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self.options = DistanceToSelectionOptions()
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def run(self, similarities, selection):
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self.show_gui(similarities, self.options)
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retval = []
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dims = similarities.get_dim_name()
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if dims[0] != "_%s" %dims[1] and dims[1] != "_%s" %dims[0]:
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logger.log('warning', 'Are you sure this is a similarity matrix?')
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dim = dims[0]
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print "dim", dim
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print "selection", selection[dim]
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print "indices", similarities.get_indices(dim, selection[dim])
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indices = similarities.get_indices(dim, selection[dim])
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m = apply_along_axis(max, 1, similarities.asarray().take(indices, 1))
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retval.append(dataset.Dataset(m, [(dim, similarities[dim]),
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("_dummy", '0')]))
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return retval
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def show_gui(self, similarities, options, edit=True):
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dialog = DistanceToSelectionOptionsDialog([similarities], self.options)
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response = dialog.run()
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dialog.hide()
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if response == gtk.RESPONSE_OK:
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dialog.set_output()
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return dialog.get_options()
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else:
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return options
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class GOWeightFunction(workflow.Function):
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def __init__(self):
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workflow.Function.__init__(self, 'load-go-ann', 'GO Influence')
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self.options = GOWeightOptions()
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def run(self, genelist, similarity):
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## Show dialog box
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self.show_gui(self.options)
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## assure that data is "correct", i.e., that we can perform
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## the desired operations.
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common_dims = genelist.common_dims(similarity)
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if len(common_dims) == 0:
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logger.log('error', 'No common dimension in the selected datasets.')
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elif len(common_dims) > 1:
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logger.log('error', "More than one common dimension in the " +
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"selected datasets. Don't know what to do.")
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gene_dim = common_dims[0]
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logger.log('debug', 'Assuming genes are in dimension: %s' % gene_dim)
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## Do the calculations.
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d = {}
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def show_gui(self, options, edit=True):
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dialog = GOWeightDialog()
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dialog.set_options(self.options)
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dialog.show_all()
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dialog.set_editable(edit)
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response = dialog.run()
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dialog.hide()
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if response == gtk.RESPONSE_OK:
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return dialog.update_options(self.options)
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else:
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return options
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class DistanceToSelectionOptionsDialog(workflow.OptionsDialog):
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def __init__(self, data, options):
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workflow.OptionsDialog.__init__(self, data, options, ['X'])
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class TTestOptionsDialog(workflow.OptionsDialog):
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def __init__(self, data, options):
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workflow.OptionsDialog.__init__(self, data, options,
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['X', 'Categories'])
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vb = gtk.VBox()
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l = gtk.Label("Limit")
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adj = gtk.Adjustment(0, 0.0, 1.0, 0.01, 1.0, 1.0)
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sb = gtk.SpinButton(adj, 0.0, 2)
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l.show()
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sb.show()
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vb.add(l)
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vb.add(sb)
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vb.show()
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self.nb.insert_page(vb, gtk.Label("Limit"), -1)
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class TTestFunction(workflow.Function):
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def __init__(self):
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workflow.Function.__init__(self, 't-test', 't-test')
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self.options = TTestOptions()
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def run(self, x, categories):
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self.show_gui(x, categories)
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retval = []
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m = x.asarray()
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c = categories.asarray()
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# Nonsmokers and current smokers
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ns = m.take(nonzero(c[:,0]), 0)[0]
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cs = m.take(nonzero(c[:,2]), 0)[0]
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tscores = stats.ttest_ind(ns, cs)
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print "Out data:", self.options['out_data']
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tds = dataset.Dataset(tscores[0], [('gene_id', x['gene_id']),
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('_t', ['0'])],
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name='t-values')
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if 't-value' in self.options['out_data']:
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retval.append(tds)
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pds = dataset.Dataset(tscores[1], [('gene_id', x['gene_id']),
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('_p', ['0'])],
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name='p-values')
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if 'p-value' in self.options['out_data']:
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retval.append(pds)
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if ProbabilityHistogramPlot in self.options['out_plots']:
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retval.append(ProbabilityHistogramPlot(pds))
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if VolcanoPlot in self.options['out_plots']:
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fc = apply_along_axis(mean, 0, ns) / apply_along_axis(mean, 0, cs)
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fcds = dataset.Dataset(fc, [('gene_id', x['gene_id']),
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('_dummy', ['0'])],
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name="Fold change")
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retval.append(VolcanoPlot(fcds, pds, 'gene_id'))
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return retval
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def show_gui(self, x, categories):
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dialog = TTestOptionsDialog([x, categories], self.options)
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response = dialog.run()
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dialog.hide()
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if response == gtk.RESPONSE_OK:
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dialog.set_output()
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return dialog.get_options()
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else:
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return options
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class PlotDagFunction(workflow.Function):
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def __init__(self):
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workflow.Function.__init__(self, 'go-dag', 'Build DAG')
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def run(self, selection):
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g = self.get_network(list(selection['go-terms']))
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# print g.edges()
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ds = dataset.GraphDataset(networkx.adj_matrix(g),
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[('go-terms', g.nodes()), ('_go-terms', g.nodes())],
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name="DAG")
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return [DagPlot(g)]
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def get_network(self, terms, subtree='bp'):
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"""Returns a DAG connecting the given terms by including their parents
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up to the level needed to connect them. The subtree parameter is one of
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mf - molecular function
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bp - biological process
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cc - cellular component"""
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rpy.r.library("GOstats")
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if subtree == 'mf':
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subtree_r = rpy.r.GOMFPARENTS
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elif subtree == 'bp':
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subtree_r = rpy.r.GOBPPARENTS
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elif subtree == 'cc':
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subtree_r = rpy.r.GOCCPARENTS
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else:
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raise Exception("Unknown subtree. Use mf, bp or cc.")
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g = rpy.r.GOGraph(terms, subtree_r)
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edges = rpy.r.edges(g)
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nxgraph = networkx.DiGraph()
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for child, d in edges.items():
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for parent in d.keys():
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nxgraph.add_edge(parent, child)
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return nxgraph
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class TTestOptions(workflow.Options):
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def __init__(self):
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workflow.Options.__init__(self)
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self['all_plots'] = [(ProbabilityHistogramPlot, 'Histogram', True),
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(VolcanoPlot, 'Histogram', True)]
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self['all_data'] = [('t-value', 't-values', True),
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('p-value', 'Probabilities', True),
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('categories', 'Categories', False)]
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self['out_data'] = ['t-value', 'p-value']
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class DistanceToSelectionOptions(workflow.Options):
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def __init__(self):
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workflow.Options.__init__(self)
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self['all_data'] = [('mindist', 'Minimum distance', True)]
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class GOWeightOptions(workflow.Options):
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def __init__(self):
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workflow.Options.__init__(self)
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self['similarity_threshold'] = 0.0
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self['rank_threshold'] = 0.0
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class ProbabilityHistogramPlot(plots.HistogramPlot):
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def __init__(self, ds):
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plots.HistogramPlot.__init__(self, ds, name="Confidence", bins=50)
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class VolcanoPlot(plots.ScatterPlot):
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def __init__(self, fold_ds, p_ds, dim, **kw):
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plots.ScatterPlot.__init__(self, fold_ds, p_ds, 'gene_id', '_dummy',
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'0', '0',
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name="Volcano plot",
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sel_dim_2='_p', **kw)
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class DagPlot(plots.Plot):
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def __init__(self, graph, dim='go-terms', pos=None, nodecolor='b', nodesize=40,
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with_labels=False, name='DAG Plot'):
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plots.Plot.__init__(self, name)
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self.nodes = graph.nodes()
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self.graph = graph
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self._pos = pos
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self._nodesize = nodesize
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self._nodecolor = nodecolor
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self._with_labels = with_labels
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self.current_dim = dim
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if not self._pos:
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self._pos = self._calc_pos(graph)
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self._xy = asarray([self._pos[node] for node in self.nodes])
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self.xaxis_data = self._xy[:,0]
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self.yaxis_data = self._xy[:,1]
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# Initial draw
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self.default_props = {'nodesize' : 50,
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'nodecolor' : 'blue',
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'edge_color' : 'gray',
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'edge_color_selected' : 'red'}
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self.node_collection = None
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self.edge_collection = None
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self.node_labels = None
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lw = zeros(self.xaxis_data.shape)
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self.node_collection = self.axes.scatter(self.xaxis_data, self.yaxis_data,
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s=self._nodesize,
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c=self._nodecolor,
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linewidth=lw,
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zorder=3)
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self._mappable = self.node_collection
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# selected nodes is a transparent graph that adjust node-edge visibility
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# according to the current selection needed to get get the selected
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# nodes 'on top' as zorder may not be defined individually
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self.selected_nodes = self.axes.scatter(self.xaxis_data,
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self.yaxis_data,
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s=self._nodesize,
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c=self._nodecolor,
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edgecolor='r',
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linewidth=lw,
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zorder=4,
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alpha=0)
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edge_color = self.default_props['edge_color']
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self.edge_collection = networkx.draw_networkx_edges(self.graph,
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self._pos,
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ax=self.axes,
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edge_color=edge_color)
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# edge color rgba-arrays
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self._edge_color_rgba = matlib.repmat(plots.ColorConverter().to_rgba(edge_color),
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self.graph.number_of_edges(),1)
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self._edge_color_selected = plots.ColorConverter().to_rgba(self.default_props['edge_color_selected'])
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if self._with_labels:
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self.node_labels = networkx.draw_networkx_labels(self.graph,
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self._pos,
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ax=self.axes)
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# remove axes, frame and grid
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self.axes.set_xticks([])
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self.axes.set_yticks([])
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self.axes.grid(False)
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self.axes.set_frame_on(False)
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self.fig.subplots_adjust(left=0, right=1, bottom=0, top=1)
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def _calc_pos(self, graph):
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"""Calculates position for graph nodes."""
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gv_graph = networkx.DiGraph()
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for start, end in graph.edges():
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gv_graph.add_edge(start.replace('GO:', ''), end.replace('GO:', ''))
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pos_gv = networkx.pygraphviz_layout(gv_graph, prog="dot")
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pos = {}
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for k, v in pos_gv.items():
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if k != "all":
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pos["GO:%s" % k] = v
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else:
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pos[k] = v
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return pos
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def rectangle_select_callback(self, x1, y1, x2, y2, key):
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ydata = self.yaxis_data
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xdata = self.xaxis_data
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# find indices of selected area
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if x1>x2:
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x1, x2 = x2, x1
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if y1>y2:
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y1, y2 = y2, y1
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assert x1<=x2
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assert y1<=y2
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index = nonzero((xdata>x1) & (xdata<x2) & (ydata>y1) & (ydata<y2))[0]
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ids = [self.nodes[i] for i in index]
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ids = self.update_selection(ids, key)
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self.selection_listener(self.current_dim, ids)
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def lasso_select_callback(self, verts, key=None):
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xys = c_[self.xaxis_data[:,newaxis], self.yaxis_data[:,newaxis]]
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index = nonzero(points_inside_poly(xys, verts))[0]
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ids = [self.nodes[i] for i in index]
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ids = self.update_selection(ids, key)
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self.selection_listener(self.current_dim, ids)
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def set_current_selection(self, selection):
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linewidth = zeros(self.xaxis_data.shape)
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edge_color_rgba = self._edge_color_rgba.copy()
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index = [i for i in range(len(self.nodes)) if self.nodes[i] in selection[self.current_dim]]
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if len(index) > 0:
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linewidth[index] = 2
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idents = selection[self.current_dim]
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edge_index = [i for i,edge in enumerate(self.graph.edges()) if (edge[0] in idents and edge[1] in idents)]
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if len(edge_index)>0:
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for i in edge_index:
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edge_color_rgba[i,:] = self._edge_color_selected
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self._A = None
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self.edge_collection._colors = edge_color_rgba
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self.selected_nodes.set_linewidth(linewidth)
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self.canvas.draw()
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